We have developed the Proteome Discovery Pipeline, a stand-alone bioinformatics platform used for LC/MS data analysis and biomarker discovery. Data is processed in a series of self-contained analytical steps using modules that are controlled by a graphical user interface. The user interface was developed in Visual C++ 6.0 and provides a multi-threaded, tabbed user interface with each tab representing a step in the analysis process. Modules included are spectrum deconvolution, alignment, normalization, significance tests and pattern recognition. Modules consist of applications developed in C++ and the R scripting language, which are called as external processes from the GUI using inputted parameters. Molecular correlation analysis can be viewed interactively using SysNet. Figure 1 shows the architecture of the Proteome Discovery Pipeline.